From what I've read, basketball throw is all about technique and practice. You'll grow a lot and get a lot of strength over the next two years, and if you do a search of these forums, you'll get a lot of tips that may help you. If you go to summer seminar, they'll give you a lot of hands on practice and tips too. But as you said, for nearly all of these, the best thing to do is practice.
When my son applied to summer seminar last December, he couldn't do a single pullup. He started practicing at home (just bought the $20 pullup bar to put in his room) and by the time he went, he did 9. After working out a bit more at home, when he took it for real he got 10. If you're starting from 5, you're way ahead of that.
Same for the pushups and situps. If you do them and practice, you'll build them slowly. He went from about 25 pushups to about 55. Situps were never a problem, but make sure you're doing them correctly. They are NOT full situps like we did back 25 year ago - your elbows only have to contact somewhere between your thigh and knee, not all the way up to your knee. He was probably doing about 70 at home, but when he went to SS and they showed him how to do them right (much easier), he easily maxed that each time he took them.
Shuttle run - again technique. You may need to do this a few times to get a good score. When my son took it at Navy SLS, he slipped each time he took it for real and got a poor score. Luckily it's one of the earlier events so if you're taking it with a PE teacher at your school, you could always redo it a different day if you just had a bad day at this. My son finally got it down to about 8.4 with practice.
Running - you know. You need to run. Only way that will improve. And as you saw, it's a killer after doing everything else. So you need to be able to run about 4 miles easily in order for that one mile to feel easy here. And then, if you go to USAFA SS, you'll STILL be dying just because of the altitude. When my son took it there he was more than a minute slower than anywhere else.
Just for reference, you want to shoot for at least the average scores. This link will give you info on those and technique/requirements if you haven't found it yet:
http://admissions.usma.edu/prospectus/CFA_Instructions05.pdf
However, just unofficially, my son knew kids at summer seminar who all compared scores, and they did tell them there (WP's) if they failed a section (these minimums aren't published officially anywhere). The other 4 scores you list were all passing there from people he knows (and of course you'll improve between now and then). The BB throw passing seemed to be 50-low (under 50 feet didn't pass). The mile seemed to be around 8 minutes. So you have some work to do there on those two, but again in 2 years, shouldn't be a problem if you do work!
) by the time he went to the other two.